GREMLIN Database
YAFK - Putative L,D-transpeptidase YafK
UniProt: P0AA99 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13148
Length: 246 (211)
Sequences: 477 (317)
Seq/√Len: 21.8

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Sco Prob
199_K203_D5.7731.00
113_I134_I4.7371.00
158_V169_V3.9061.00
110_Y152_D3.7781.00
137_D148_N3.6651.00
132_L144_Y3.5041.00
74_C138_C3.2341.00
117_F132_L3.1391.00
197_Q223_V3.0501.00
115_I171_V2.9730.99
179_T182_N2.9520.99
104_K112_A2.8870.99
51_E185_R2.8340.99
47_Q58_Y2.7360.99
54_T72_K2.7270.99
146_M154_I2.6760.99
122_D127_Y2.6290.99
103_L158_V2.4700.98
68_L157_F2.4590.98
46_I204_Y2.2780.96
45_Y211_P2.1770.95
182_N186_H2.1230.95
48_I144_Y2.0910.94
59_V68_L2.0810.94
86_Q130_K2.0710.94
176_F182_N1.9990.93
209_R224_S1.9450.92
44_V158_V1.8910.90
117_F151_I1.8240.89
191_F194_F1.8080.88
197_Q200_P1.7990.88
79_G90_K1.7390.86
47_Q172_S1.7370.86
204_Y208_T1.7230.86
115_I132_L1.6420.83
200_P223_V1.6080.81
57_L157_F1.5750.80
210_K213_T1.5740.80
133_M144_Y1.5510.79
214_V223_V1.5490.79
178_M182_N1.5320.78
84_Q127_Y1.4880.76
48_I55_L1.4710.75
58_Y157_F1.4420.74
121_Y127_Y1.4210.72
54_T70_S1.4090.72
50_K81_G1.3420.68
44_V160_G1.3320.67
25_S29_T1.3130.66
144_Y173_I1.2930.65
45_Y172_S1.2880.65
73_I122_D1.2870.65
32_S36_K1.2760.64
113_I128_E1.2710.64
29_T32_S1.2650.63
22_L26_S1.2410.62
98_V115_I1.2330.61
192_K195_W1.2240.61
176_F179_T1.2240.61
57_L103_L1.2140.60
78_G153_E1.1990.59
161_A219_G1.1980.59
99_Q102_Q1.1810.58
104_K107_S1.1800.58
45_Y212_P1.1730.57
102_Q168_S1.1730.57
86_Q127_Y1.1600.56
110_Y151_I1.1570.56
47_Q206_E1.1540.56
73_I146_M1.1500.56
178_M183_M1.1410.55
137_D145_A1.1300.54
78_G90_K1.1260.54
191_F195_W1.1170.54
86_Q131_Y1.1100.53
121_Y125_H1.1000.52
123_R134_I1.0950.52
44_V161_A1.0900.52
89_F139_V1.0850.51
89_F141_I1.0780.51
95_F201_G1.0740.51
84_Q121_Y1.0590.50
224_S227_L1.0270.47
139_V171_V1.0260.47
20_G23_G1.0250.47
174_Y212_P1.0240.47
114_N133_M1.0210.47
128_E134_I1.0040.46
102_Q115_I0.9940.45
91_S132_L0.9930.45
21_L24_S0.9900.45
116_G146_M0.9880.45
120_A123_R0.9830.44
72_K150_G0.9800.44
46_I67_L0.9770.44
100_R127_Y0.9700.44
20_G24_S0.9660.43
201_G223_V0.9580.43
19_A22_L0.9540.43
117_F130_K0.9510.42
161_A166_Q0.9470.42
195_W221_Y0.9400.42
81_G93_E0.9320.41
204_Y223_V0.9220.40
50_K93_E0.9100.40
113_I133_M0.9050.39
176_F186_H0.9030.39
149_Q162_L0.9020.39
43_P116_G0.8990.39
78_G175_P0.8990.39
100_R131_Y0.8940.39
117_F163_V0.8850.38
48_I112_A0.8780.38
134_I169_V0.8770.38
23_G46_I0.8740.37
163_V218_N0.8710.37
91_S133_M0.8620.37
156_Q159_T0.8600.36
44_V166_Q0.8590.36
32_S39_L0.8550.36
48_I91_S0.8550.36
68_L97_S0.8530.36
121_Y146_M0.8300.35
57_L131_Y0.8230.34
193_D214_V0.8200.34
169_V175_P0.8180.34
112_A139_V0.8170.34
138_C221_Y0.8130.34
93_E175_P0.8130.34
98_V169_V0.8120.33
63_E72_K0.8080.33
128_E133_M0.8070.33
114_N144_Y0.8000.33
76_Y91_S0.7980.33
132_L186_H0.7970.33
75_K90_K0.7950.32
147_T165_G0.7940.32
71_Y153_E0.7920.32
116_G133_M0.7890.32
181_A185_R0.7890.32
45_Y223_V0.7840.32
188_Y192_K0.7770.31
23_G26_S0.7710.31
26_S30_P0.7680.31
114_N140_S0.7670.31
108_R149_Q0.7640.31
61_M112_A0.7640.31
58_Y90_K0.7630.31
41_G98_V0.7620.31
49_F56_D0.7600.30
35_Y112_A0.7540.30
145_A171_V0.7490.30
139_V151_I0.7490.30
202_Y206_E0.7400.29
28_T130_K0.7370.29
83_K88_D0.7360.29
92_P142_G0.7360.29
83_K92_P0.7360.29
94_G118_P0.7360.29
83_K142_G0.7360.29
88_D135_H0.7360.29
83_K135_H0.7360.29
94_G129_G0.7360.29
94_G135_H0.7360.29
94_G142_G0.7360.29
83_K94_G0.7360.29
83_K129_G0.7360.29
118_P129_G0.7360.29
92_P135_H0.7360.29
92_P129_G0.7360.29
129_G142_G0.7360.29
88_D142_G0.7360.29
88_D129_G0.7360.29
88_D118_P0.7360.29
88_D94_G0.7360.29
88_D92_P0.7360.29
118_P142_G0.7360.29
135_H142_G0.7360.29
129_G135_H0.7360.29
118_P135_H0.7360.29
92_P118_P0.7360.29
83_K118_P0.7360.29
33_K68_L0.7330.29
57_L106_D0.7260.29
18_F26_S0.7240.28
212_P221_Y0.7160.28
69_D180_D0.7150.28
114_N154_I0.7050.27
176_F195_W0.7050.27
89_F206_E0.7040.27
97_S169_V0.7030.27
55_L72_K0.7030.27
82_P175_P0.7010.27
23_G181_A0.7010.27
40_M132_L0.6980.27
147_T166_Q0.6970.27
138_C175_P0.6920.27
61_M117_F0.6900.27
58_Y206_E0.6890.27
37_Q61_M0.6870.26
121_Y131_Y0.6830.26
87_G136_G0.6830.26
180_D184_K0.6770.26
46_I74_C0.6760.26
91_S130_K0.6720.26
113_I116_G0.6710.26
102_Q146_M0.6690.25
204_Y207_Q0.6650.25
101_N171_V0.6640.25
61_M66_Q0.6580.25
135_H143_C0.6570.25
92_P143_C0.6570.25
88_D143_C0.6570.25
129_G143_C0.6570.25
118_P143_C0.6570.25
83_K143_C0.6570.25
94_G143_C0.6570.25
77_S90_K0.6550.25
121_Y140_S0.6550.25
55_L154_I0.6520.25
69_D153_E0.6470.24
42_S158_V0.6460.24
100_R103_L0.6450.24
59_V159_T0.6430.24
125_H216_V0.6310.24
103_L162_L0.6280.23
99_Q168_S0.6230.23
26_S168_S0.6230.23
122_D129_G0.6230.23
88_D122_D0.6230.23
118_P122_D0.6230.23
94_G122_D0.6230.23
92_P122_D0.6230.23
83_K122_D0.6230.23
122_D135_H0.6230.23
122_D142_G0.6230.23
78_G95_F0.6230.23
22_L25_S0.6190.23
175_P178_M0.6190.23
103_L159_T0.6140.23
54_T193_D0.6140.23
120_A152_D0.6110.23
107_S158_V0.6090.23
17_S21_L0.6080.22
81_G95_F0.6030.22
161_A175_P0.6010.22
36_K209_R0.6010.22
89_F184_K0.5990.22
132_L163_V0.5960.22
204_Y209_R0.5960.22
137_D161_A0.5920.22
100_R163_V0.5900.22
122_D131_Y0.5880.22
172_S214_V0.5860.21
54_T207_Q0.5810.21
187_K196_E0.5810.21
140_S145_A0.5810.21
37_Q209_R0.5790.21
168_S220_R0.5790.21
32_S35_Y0.5740.21
63_E191_F0.5740.21
204_Y219_G0.5720.21
78_G103_L0.5720.21
174_Y202_Y0.5700.21
102_Q117_F0.5690.21
54_T173_I0.5690.21
174_Y179_T0.5680.21
74_C77_S0.5670.21
93_E105_P0.5660.21
140_S162_L0.5650.20
38_Q173_I0.5650.20
148_N151_I0.5640.20
107_S155_F0.5640.20
137_D151_I0.5620.20
194_F201_G0.5560.20
141_I191_F0.5550.20
95_F174_Y0.5500.20
69_D85_R0.5490.20
51_E70_S0.5450.20
73_I121_Y0.5440.20
145_A169_V0.5420.19
162_L167_P0.5380.19
76_Y90_K0.5370.19
77_S175_P0.5330.19
181_A210_K0.5330.19
92_P119_N0.5330.19
88_D119_N0.5330.19
119_N142_G0.5330.19
119_N135_H0.5330.19
119_N129_G0.5330.19
83_K119_N0.5330.19
94_G119_N0.5330.19
104_K153_E0.5330.19
103_L145_A0.5320.19
140_S146_M0.5300.19
203_D223_V0.5290.19
101_N219_G0.5290.19
91_S131_Y0.5250.19
144_Y154_I0.5200.19
44_V165_G0.5190.19
121_Y128_E0.5160.18
19_A130_K0.5160.18
97_S134_I0.5150.18
113_I140_S0.5120.18
96_Y117_F0.5100.18
60_K65_Y0.5100.18
97_S102_Q0.5070.18
23_G63_E0.5060.18
41_G57_L0.5060.18
147_T185_R0.5060.18
25_S219_G0.5050.18
109_Y224_S0.5050.18
75_K213_T0.5040.18
42_S60_K0.5030.18
123_R170_Q0.5020.18
109_Y127_Y0.5000.18
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

HHsearch Results:
Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov % HHΔ  
4xxtA 1 0.5854 99.6 0.795 Contact Map
4k73A 1 0.6057 99.6 0.795 Contact Map
3vypA 1 0.7358 99.6 0.801 Contact Map
4xvoA 1 0.622 99.6 0.803 Contact Map
4qtfA 2 0.7317 99.6 0.803 Contact Map
1zatA 1 0.5976 99.6 0.804 Contact Map
4jmnA 1 0.6179 99.6 0.806 Contact Map
4lzhA 1 0.8496 99.6 0.808 Contact Map
4a1kA 2 0.5854 99.5 0.811 Contact Map
4lpqA 1 0.6098 99.5 0.811 Contact Map

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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